LFNG LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase [Homo sapiens (human)] - Gene

Summary

Official Symbol: LFNGprovided by HGNC
Official Full Name: LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferaseprovided by HGNC
Primary source: HGNC:HGNC:6560
See related: Ensembl:ENSG00000106003 MIM:602576; AllianceGenome:HGNC:6560
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SCDO3
Summary: This gene is a member of the glycosyltransferase 31 gene family. Members of this gene family, which also includes the MFNG (GeneID: 4242) and RFNG (GeneID: 5986) genes, encode evolutionarily conserved glycosyltransferases that act in the Notch signaling pathway to define boundaries during embryonic development. While their genomic structure is distinct from other glycosyltransferases, these proteins have a fucose-specific beta-1,3-N-acetylglucosaminyltransferase activity that leads to elongation of O-linked fucose residues on Notch, which alters Notch signaling. The protein encoded by this gene is predicted to be a single-pass type II Golgi membrane protein but it may also be secreted and proteolytically processed like the related proteins in mouse and Drosophila (PMID: 9187150). Mutations in this gene have been associated with autosomal recessive spondylocostal dysostosis 3. [provided by RefSeq, May 2018]
Expression: Ubiquitous expression in skin (RPKM 16.6), stomach (RPKM 14.0) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7p22.3

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (2512529..2529177)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (2625971..2642596)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (2552163..2568811)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of bi-allelic LFNG variants in three patients and further clinical and molecular refinement of spondylocostal dysostosis 3.
Title: Identification of bi-allelic LFNG variants in three patients and further clinical and molecular refinement of spondylocostal dysostosis 3.
Lunatic fringe promotes the aggregation of CADASIL NOTCH3 mutant proteins.
Title: Lunatic fringe promotes the aggregation of CADASIL NOTCH3 mutant proteins.
Bioinformatics and Functional Analyses Implicate Potential Roles for EOGT and L-fringe in Pancreatic Cancers.
Title: Bioinformatics and Functional Analyses Implicate Potential Roles for EOGT and L-fringe in Pancreatic Cancers.
LFNG mutation is associated with spondylocostal dysostosis.
Title: Identification of novel LFNG mutations in spondylocostal dysostosis.
LFNG expression plays a functional role in regulating melanoma metastasis.
Title: Comparative genomics reveals that loss of lunatic fringe (LFNG) promotes melanoma metastasis.
Genetic interaction between lunatic fringe and TP53 was identified in breast cancer tumorigenesis.
Title: Lunatic Fringe and p53 Cooperatively Suppress Mesenchymal Stem-Like Breast Cancer.
a potent tumor-suppressive function for Lfng
Title: Lunatic Fringe is a potent tumor suppressor in Kras-initiated pancreatic cancer.
TGFBR2 signaling can affect Notch1 glycosylation via regulation of glycosyltransferase LFNG expression and provide a first mechanistic example for altered glycosylation in microsatellite instability colorectal tumor cells.
Title: Reconstitution of TGFBR2 in HCT116 colorectal cancer cells causes increased LFNG expression and enhanced N-acetyl-d-glucosamine incorporation into Notch1.
LFNG expression correlates with expansion of cancer stem cell populations and NKX3.1 expression in human prostate cancer.
Title: Tumor-suppressive activity of Lunatic Fringe in prostate through differential modulation of Notch receptor activation.
Reduced LFNG expression facilitates JAG/NOTCH luminal progenitor signaling and cooperates with MET/CAVEOLIN basal-type signaling to promote basal-like breast cancer.
Title: Lunatic fringe deficiency cooperates with the Met/Caveolin gene amplicon to induce basal-like breast cancer.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Spondylocostal dysostosis MedGen: C0265343 GeneReviews: Spondylocostal Dysostosis, Autosomal Recessive	Compare labs
Spondylocostal dysostosis 3, autosomal recessive MedGen: C1853296 OMIM: 609813 GeneReviews: Spondylocostal Dysostosis, Autosomal Recessive	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-15937 (e-PCR)
- UniSTS:9218

D7S2257 (e-PCR)
- UniSTS:153609

D7S2382E (e-PCR)
- UniSTS:153918

MARC_26643-26644:1036437678:1 (e-PCR)
- UniSTS:269049

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity	TAS Traceable Author Statement more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in animal organ morphogenesis	NAS Non-traceable Author Statement more info	PubMed
involved_in compartment pattern specification	IEA Inferred from Electronic Annotation more info
involved_in marginal zone B cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of Notch signaling pathway involved in somitogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in ovarian follicle development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of Notch signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of meiotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in regulation of Notch signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of Notch signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of somitogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in somitogenesis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in Golgi membrane	TAS Traceable Author Statement more info
located_in extracellular region	NAS Non-traceable Author Statement more info	PubMed
located_in extracellular vesicle	HDA more info	PubMed

General protein information

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Preferred Names: beta-1,3-N-acetylglucosaminyltransferase lunatic fringe

NP_001035257.1

EC 2.4.1.222

NP_001035258.1

EC 2.4.1.222

NP_001159827.1

EC 2.4.1.222

NP_002295.1

EC 2.4.1.222

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008109.2 RefSeqGene

Range

12246..20901

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001040167.2 → NP_001035257.1 beta-1,3-N-acetylglucosaminyltransferase lunatic fringe isoform a

See identical proteins and their annotated locations for NP_001035257.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AC092488, BC014851, BM854210, U94354

Consensus CDS

CCDS34587.1

UniProtKB/Swiss-Prot

B3KTY6, B5MCR5, O00589, Q8NES3, Q96C39, Q9UJW5

Related

ENSP00000222725.5, ENST00000222725.10

Conserved Domains (1) summary

pfam02434
Location:110 → 358

Fringe; Fringe-like
NM_001040168.2 → NP_001035258.1 beta-1,3-N-acetylglucosaminyltransferase lunatic fringe isoform b

See identical proteins and their annotated locations for NP_001035258.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) includes an alternate 3' terminal exon compared to variant 1. The resulting protein (isoform b) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC092488, AF193612, U94354

Consensus CDS

CCDS34586.1

UniProtKB/Swiss-Prot

Q8NES3

Related

ENSP00000352579.3, ENST00000359574.7

Conserved Domains (1) summary

pfam02434
Location:110 → 358

Fringe; Fringe-like
NM_001166355.2 → NP_001159827.1 beta-1,3-N-acetylglucosaminyltransferase lunatic fringe isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3) has multiple differences, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate start codon, compared to variant 1. The encoded protein (isoform c) has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AK096284, BC014851

Consensus CDS

CCDS55081.1

UniProtKB/Swiss-Prot

Q8NES3

Related

ENSP00000385764.1, ENST00000402506.5

Conserved Domains (1) summary

pfam02434
Location:72 → 287

Fringe; Fringe-like
NM_002304.3 → NP_002295.1 beta-1,3-N-acetylglucosaminyltransferase lunatic fringe isoform d

See identical proteins and their annotated locations for NP_002295.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) has multiple differences, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate start codon, compared to variant 1. The encoded protein (isoform d) has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AK096284, BC014851

Consensus CDS

CCDS55082.1

UniProtKB/Swiss-Prot

Q8NES3

Related

ENSP00000384786.1, ENST00000402045.5

Conserved Domains (1) summary

pfam02434
Location:16 → 229

Fringe; Fringe-like

RNA

NR_178195.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) represents an alternate non-coding allele of variant 3 on T2T-CHM13v2.0 genome assembly. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

CP068271